Tag: Phylogenomics

This is a guest post by Amir Szitenberg, a postdoc in my lab @EvoHull, describing a phylogenomic investigation using ReproPhylo. Amir used to be a sponge researcher if you can’t tell from the tone below. Despite already knowing ReproPhylo could do all this rapidly and of course reproducibly, I was still both surprised and impressed by the scale and speed…

This is a guest post by Amir Szitenberg, postdoctoral researcher in my group at the University of Hull, and main author of @ReproPhylo I find the ReproPhylo approach to experimental phylogenomics very exciting, and can see how it would lead to better, in depth understanding of phylogenomic datasets, regardless of their size. An example for this…

Our new phylogenomics environment is called ReproPhylo. It makes experimental reproducibility frictionless, occurring quietly in the background while you work on the science. The environment has a lot of tools to allow exploration of phylogenomics data and to create phylogenomic analysis pipelines. It is distributed in a Docker container simplifying installation and allowing the reproducibility…

I’ve been reading a lot recently about reproducible research (RR) in bioinformatics on several blogs, and Google+ and Twitter. The idea is that it is important that someone is easily able to reproduce* your results (and even figures) from your publication using your provided code and data. I’ve been thinking that this is a movement…

While I was reading the Nature paper I was talking about in my last post I was thinking about the use of the term “phylogenomics”. It seems like there are two quite separate contexts where it is used.(1) Integrating evolutionary biology into genomics (2) phylogenetics using a lot of data The term “phylogenomics” was first…